Modified oligonucleotides which possess at least one substituted 7-deazapurine base form more stable hybridization complexes with nucleic acids than unsubstituted analogs. They are useful as inhibitors of gene expression, as probes for detecting nucleic acids, as aids in molecular biology and as pharmaceuticals...http://www.google.com/patents/US6479651?utm_source=gb-gplus-sharePatent US6479651 - Modified oligonucleotides, their preparation and their use

Modified oligonucleotides, their preparation and their useUS 6479651 B1

Abstract

Modified oligonucleotides which possess at least one substituted 7-deazapurine base form more stable hybridization complexes with nucleic acids than unsubstituted analogs. They are useful as inhibitors of gene expression, as probes for detecting nucleic acids, as aids in molecular biology and as pharmaceuticals or diagnostic agents. Processes for preparing them are provided.

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Claims(14)

What is claimed:

1. An oligonucleotide of the formula I

or a physiologically acceptable salt thereof, in which

B is, independently of each other, a base which is customary in nucleotide chemistry, and at least on B is a base of the formula II

in which

R15 and R16 are, independently of each other,

(1.) hydrogen,

(2.) halogen,

(3.) (C1-C10)-alkyl,

(4.) (C1-C10)-alkenyl,

(5.) (C1-C10)-alkynyl,

(6.) NO2,

(7.) NH2,

(8.) cyano,

(9.) —S—(C1-C5)-alkyl,

(10.) (C1-C5)-alkoxy,

(11.) (C5-C20)-aryloxy,

(12.) SiH3,

(13.)

(14.) a radical as described under (3.), (4.), or (5.) which is substituted by one or more radicals selected from the group consisting of SH, —S—(C1-C6)-alkyl, (C1-C6)-alkoxy, OH, —NR(c)R(d), —CO—R(b), —NH—CO—NR(c)R(d), —NR(c)R(g), —NR(e)R(f), and —NR(e)R(g), or by a polyalkyleneglycol radical of the formula —[O—(CH2)r]s,—NR(c)R(d), where r and s are, independently of each other an integer between 1 to 18, wherein any of the foregoing OH, SH, —CO—R(b), —NH—CO—NR(c)R(d), —NR(c)R(d), —NR(e)R(f), and —NR(e)R(g) or —NR(c)R(g) groups which favor intracellular uptake or serve as labeling for a DNA or RNA probe or, when the oligonucleotide analog hybridizes to the target mucleic acid, attack the latter while binding, cross-linking or cleaving, or

(15.) are a radical as defined under (3.), (4.), or (5.) in which from one to all the H atoms are substituted by halogen;

R(a) is OH, (C1-C5)-alkoxy, (C5-C20)-aryloxy, NH2 or NH—T, where T is an alkylcarboxyl group or alkylamino group which is linked to one or more groups, where appropriate via a further linker, which intra-cellular uptake or serve for labeling a DNA or RNA probe or, when the oiigonucleotide analog hybridizes to the target nucleic acid, attack the latter while binding, cross-linking or cleaving,

R(b) is hydroxyl, (C1-C6)-alkoxy or —NR(c)R(d),

R(c) and R(d) are, independently of each other, H or (C1-C6)-alkyl which is unsubstituted or substituted by —NR(e)R(f) or —NR(e)R(g),

R(e) and R(f) are, independently of each other, H or (C1-C6)-alkyl,

R(g) is (C1-C6)-alkyl-COOH;

with the proviso that when R15 and R16 are identical, they cannot by hydrogen, NO2, NH2, cyano or SiH3;

E and F are, independently of each other, H, OH, or NH2,

R1 is hydrogen, (C1-C18)alkyl, (C2-C19)-alkenyl, (C2-C18)-alkynyl, (C2-C18)-alkylcarbonyl, (C3-C19)-alkenylcarbonyl, (C3-C19)-alkynylcarbonyl, (C6-C14)-aryl-(C1-C8)-alkyl, a protective group which is customary in nucleotide chemistry, or a radical of the formula IIIa

R3 is C1-C18-alkyl, C6-C20-aryl, (C6-C24)-aryl-(C1-C8)-alkyl, —(CH2)c—[NH(CH2)c]d—NR6R6, in which c is an integer from 2 to 6 and each and d is an integer from 0 to 6, and each R6 is, independently, hydrogen or C1-C6-alkyl or C1-C4-alkoxy-C1-C6-alkyl;

R4 is C1-C18-alkyl, C5-C20-aryl or (C6-C10)-aryl-(C1-C8)-alkyl, or, in the case of NR3R4, is, together with R3 and the nitrogen atom carrying them, a 5-6-membered heterocyclic ring which can additionally contain a further O, S or N, heteroatom,

p is an integer from 1 to 100,

q is an integer from 0 to 22,

R5 is hydrogen or is a substituent selected from the group consisting of hydroxyl, amino, C1-C18-alkylamino, COOH, CONH2, COO(C1-C4)-alkyl or halogen;

Z and Z′ are, independently of each other, hydroxyl, mercapto, SeH, C1-C22-alkoxy, —O—(CH2)b—NR6R7, in which b is an integer from 1 to 6, and R7 is C1-C6-alkyl or R6 and R7, together with the nitrogen atom carrying them form a 3-6-membered ring, C1-C18-alkyl, C6-C20-aryl, (C6-C14)-aryl-(C1-C8)-alkyl, (C6-C14)-aryl-(C1-C8)-alkoxy, where aryl includes heteroaryl and any aryl is optionally substituted by 1, 2 or 3 identical or different radicals selected from the group consisting of carboxyl, amino, nitro, C1-C4-alkylamino, C1-C6-alkoxy, hydroxyl, halogen and cyano, C1-C18-alkylmercapto, NHR3, NR3R4, a radical or the formula IV, or a group which favors intracellular uptake or serves for labeling a DNA or RNA probe or, when the oligo-nucleotide analog hybridizes to the target nucleic acid, attacks the latter while binding, cross-linking or cleaving,

and the curved bracket indicates that R2 and the adjacent phosphoryl or —Y′—R1a radical can either be located in the 2′ and 3′ position or else, conversely, in the 3′ and 2′ position, with it being possible for each nucleotide to be present in its D or L configuration, and for the base B to be located in the α or β position.

2. An oligonucleotide as claimed in claim 1, wherein R15 is

(1.) NO2,

(2.) NH2,

(3.) —S—(C1-C6)-alkyl,

(4.) (C1-C6)-alkoxy,

(5.) (C6-C20)-aryloxy,

(6.) SiH3,

(7.)

(8.) (C1-C10)-alkyl, (C2-C10)-alkenyl or (C2-C10)-alkynyl which is substituted by one or more radicals from the group SH, —S—(C1-C6)-alkyl, (C1-C6)-alkoxy, OH, —NR(c)R(d), —CO—R(b), —NH—CO—NR(c)R(d), —NR(c)R(g), —NR(e)R(f), or —NR(e)R(g), or by a polyalkylene glycol radical of the formula —[O—(CH2)r]s—NR(c)R(d), where r and s are, independently of each other an integer between 1 to 18, with it being possible for functional groups selected from the group consisting of OH, SH, —CO—R(b), —NH—CO—NR(c)R(d), —NR(c)R(d), —NR(e)R(f), and —NR(e)R(g) and —NR(c)R(g) additionally to be linked to one or more groups, where appropriate via a further linker, which favor intracellular uptake or serve for labeling a DNA or RNA probe, when the oligonucleotide analog hybridizes to the target nucleic acid, attack the latter while binding, crosslinking or cleaving, or

(9.) (C1-C10)-alkyl, (C2-C10)-alkenyl or (C2-C10)-alkynyl in which from one to all the H atoms are substituted by halogen; and

R16 is hydrogen.

3. An oligonucleotide as claimed in claim 2, wherein R15 is (C1-C10)-alkyl, (C2-C10)-alkenyl or (C2-C10)-alkynyl in which from one to all the H atoms are substituted by halogen, and said halogen is fluorine.

4. An oligonucleotide as claimed in claim 1, wherein the base B is located in the β position, the nucleotides are present in the D configuration, R2 is located in the 2′ position, a is oxy and n is an integer from 2 to 99.

5. An oligonucleotide as claimed in claim 1, wherein

R1 is hydrogen, C1-C6-alkyl, or a radical of the formula IIIa;

R1a is hydrogen, C1-C6-alkyl, or a radical of the formula IIIb;

R2 is hydrogen, C1-C6-alkoxy, C1-C6-alkenyloxy, or hydroxyl;

n is an integer from 4 to 39;

m is an integer from 1 to 6;

U is hydroxyl, mercapto, C1-C6-alkoxy, C1-C6-alkyl, NR3R4 or NHR3, or C1-C6-alkyl, in which

R3 is C1-C8-alkyl, or methoxyethyl,

and B, W, V, Y, Y′, X and Z are as defined in claim 1.

6. An oligonucleotide as claimed in claim 5, wherein R1 and R1a are methyl; R2 is hydrogen; n is an integer from 5 to 29; m is 1; U is hydroxyl; and R3 is C1-C4-alkyl.

7. An oligonucleotide as claimed in claim 1, wherein V, Y and Y′ are oxy, sulfanediyl or imino, and W is oxo or thioxo.

8. An oligonucleotide as claimed in claim 1, wherein U is hydroxyl, methyl or mercapto.

9. An oligonucleotide as claimed in claim 1, wherein at least one of R1 and R1a is hydrogen.

10. An oligonucleotide as claimed in claim 1, wherein one or both of R15 and R16 is/are —[O—(CH2)r]s—NR(c)R(d); and r and s are, independently of each other, an integer from 1 to 6.

11. An oligonucleotide as claimed in claim 1, wherein one or both of R15 and R16 is/are a radical as defined under (3.), (4.), or (5.) in which from one to all the H atoms are substituted by halogen.

12. A diagnostic reagent, comprising at least one oligonucleotide as claimed in claim 1, together with one or more of a solid support to which it is bound, a solvent or diluent, and a diagnostically relevant auxiliary reagent.

13. A pharmaceutical composition, comprising at least one oligonucleotide as claimed in claim 1, together with a physiologically acceptable excipient.

14. An oligonucleotide as claimed in claim 1, wherein R2 is allyloxy.

Description

The instant application is a continuation of U.S. Ser. No. 09/144,112, filed Aug. 31, 1998, now U.S. Pat. No. 6,150,510, issued Nov. 21, 2000, which is a continuation of U.S. Ser. No. 08/554,164, filed Nov. 6, 1995 now U.S. Pat. No. 5,844,106, issued Dec. 1, 1998.

BACKGROUND OF THE INVENTION

The present invention relates to novel oligonucleotides which contain modified bases and which possess valuable physical, biological and pharmacological properties, to a process for their preparation and to their use as inhibitors of gene expression (antisense oligonucleotides, ribozymes, sense oligonucleotides and triplex-forming oligonucleotides), as probes for detecting nucleic acids, as aids in molecular biology and as pharmaceuticals or diagnostic agents.

Numerous chemical modifications of oligonucleotides are known from the literature. These modifications can affect the sugar-phosphate skeleton or the nucleotide bases. Reviews of the state of the art are provided, for example, by Uhlmann & Peyman, Chem. Rev. 1990, 90, 543 and Milligan et al., J. Med. Chem. 1993, 36, 1923.

As a rule, it is necessary to modify oligonucleotides chemically since unmodified oligonucleotides are very rapidly degraded by nucleolytic activities both in cells and in the cell culture medium. Stabilization against nucleolytic degradation can be achieved by replacing the sugar-phosphate backbone or by modifying the phosphate bridge, the sugar moiety or the nucleotide base [Milligan et al., above and Uhlmann & Peyman, above].

In addition to modifications which lead to oligonucleotides which possess increased stability towards nucleolytic degradation, those modifications are also of interest which alter the hybridization behavior of the modified oligonucleotides such that the latter are able, for example, to form more stable hybridization complexes (duplexes) with intracellular nucleic acids (so-called target nucleic acids). It is possible to alter the hybridization properties of oligonucleotides by, for example, modifying the bases. The altered hybridization properties of oligonucleotides which have been modified in this way can be recognized, for example, from the melting temperatures (Tm values) of the duplexes, which temperatures are different from those obtained with the unmodified oligonucleotides.

In addition, PCT Application WO 93/10820 discloses oligonucleotides which contain modified uracil or cytosine bases and which are able to form duplex or triplex structures with the target nucleic acids which are more stable than those formed by the unmodified oligonucleotides. Oligonucleotides which contain the base analog 2-aminoadenine have also been reported to exhibit improved hybridization properties [Chollet et al., (1988), Nucleic Acid Research, 16, 305-317]. German Patent Application P4415370.8 discloses that incorporating 8-azapurine bases into oligonucleotides increases the stability of the corresponding hybridization complexes with the target nucleic acids. In addition WO 93/09127 discloses oligonucleotides which contain substituted or unsubstituted 7-deazapurine bases and which, as a result, are more readily able to form triplex structures with the target molecules (double-stranded DNA). Oligonucleotides which contain 7-deazapurine bases which are substituted in the 7 position are also disclosed in WO 94/22892 and WO 94/24144.

However, it is not possible to predict the base modifications which will lead to an increase in duplex stability. Thus, numerous examples are known of base modifications which diminish duplex stability. Thus, PCT Application WO 92/002258 describes pyrimidine-modified oligonucleotides which exhibit decreased binding affinity for the target nucleic acids. Methyl or bromine substituents which are introduced at the 8 position of the purine ring also decrease the stability of the corresponding duplexes [E. N. Kanaya et al., Biochemistry (1987) 26 7159, and Biochemistry, 1984, 23, 4219]. Oligonucleotides which contain 7-deazaadenine form significantly fewer stable duplexes with complementary oligonucleotides than do oligonucleotides which contain adenine [Seela et al., Nucleic Acid Research (1982) 10, 1389].

SUMMARY OF THE INVENTION

The object of the present invention is, therefore, to make available novel oligonucleotides which possess advantageous properties.

It has now been found, surprisingly, that oligonucleotides which possess at least one substituted 7-deazapurine base form hybridization complexes with the target nucleic acids which are significantly more stable than those formed by comparable oligonucleotides which possess unsubstituted 7-deazapurine bases.

The invention consequently relates to oligonucleotides of the formula I

and the physiologically tolerated salts thereof, in which

B are, independently of each other, a base which is customary in nucleotide chemistry, and at least one B is a base of the formula II

in which

R15 and R16 are, independently of each other,

1. hydrogen,

2. halogen,

3. (C1-C10)-alkyl,

4. (C2-C13)-alkenyl,

5. (C2-C10)-alkynyl,

6. NO2,

7. NH2,

8. cyano,

9. —S—(C1-C6)-alkyl,

10. (C1-C6)-alkoxy,

11. (C6-C20)-aryloxy,

12. SiH3,

13.

14. a radical as described under 3., 4. or 5. which is substituted by one or more radicals from the group SH, S—(C1-C6)-alkyl, (C1-C6)-alkoxy, OH, —NR(c)R(d), —CO—R(b), —NH—CO—NR(c)R(d), —NR(c)R(g), —NR(e)R(f) or —NR(e)R(g), or by a polyalkyleneglycol radical of the formula —[O—(CH2)r]s—NR(c)R(d), where r and s are, independently of each other, an integer between 1 and 18, preferably between 1 and 6, with it being possible for functional groups such as OH, SH, —CO—R(b), —NH—CO—NR(c)R(d), —NR(c)R(d), —NR(e)R(f), —NR(e)R(g) or —NR(c)R(g) additionally to be linked to one or more groups, where appropriate via a further linker, which favor intracellular uptake or serve for labeling a DNA or RNA probe, or, when the oligonucleotide analog hybridizes to the target nucleic acid, attack the latter while binding, cross-linking or cleaving, or

15. a radical as defined under 3., 4. or 5. in which from one to all the H atoms are substituted by halogen, preferably fluorine;

R(a) is OH, (C1-C6)-alkoxy, (C6-C20)-aryloxy, NH2 or NH—T, where T is an alkylcarboxyl group or alkylamino group which is linked to one or more groups, where appropriate via a further linker, which favor intracellular uptake or serve for labeling a DNA or RNA probe or, when the oligonucleotide analog hybridizes to the target nucleic acid, attack the latter while binding, cross-linking or cleaving, R(b) is hydroxyl, (C1-C6)-alkoxy or —NR(c)R(d), R(c) and R(d) are, independently of each other, H or (C1-C6)-alkyl which is unsubstituted or substituted by —NR(e)R(f) or —NR(e)R(g), R(e) and R(f) are, independently of each other, H or (C1-C6)-alkyl, R(g) is (C1-C6)-alkyl-COOH; with the proviso that R15 and R16 cannot each simultaneously be hydrogen, NO2, NH2, cyano or SiH3;

E and F are, independently of each other, H, OH or NH2,

R1 is hydrogen, C1-C18-alkyl, C2-C18-alkenyl, C2-C18-alkynyl, C2-C18-alkylcarbonyl, C3-C19-alkenylcarbonyl, C3-C19-alkynylcarbonyl, (C6-C14)-aryl (C1-C8)-alkyl, a protective group which is customary in nucleotide chemistry, or a radical of the formula IIIa

R3 is C1-C18-alkyl, C6-C20-aryl, (C6-C14)-aryl-(C1-C8)-alkyl, —(CH2)c—[NH(CH2)c]d—NR6R6, in which c is an integer from 2 to 6 and d is an integer from 0 to 6, and R6 is, independently of each other, hydrogen or C1-C6-alkyl or C1-C4-alkoxy-C1-C6-alkyl;

R4 is C1-C18-alkyl, C6-C20-aryl or (C6-C10)-aryl-(C1-C8)-alkyl, or, in the case of NR3R4, is, together with R3 and the nitrogen atom carrying them, a 5-6-membered heterocyclic ring which can additionally contain a further heteroatom from the series O, S and N,

p is an integer from 1 to 100,

q is an integer from 0 to 22,

R5 is hydrogen or a functional group such as, for example, hydroxyl, amino, C1-C18-alkylamino, COOH, CONH2, COO(C1-C4)-alkyl or halogen;

Z and Z′ are, independently of each other, hydroxyl, mercapto, SeH, C1-C22-alkoxy, —O—(CH2)b—NR6R7, in which b is an integer from 1 to 6, and R7 is C1-C6-alkyl or R6 and R7, together with the nitrogen atom carrying them, form a 3-6-membered ring, C1-C18-alkyl, C6-C20-aryl, (C6-C14)-aryl-(C1-C8)-alkyl, (C6-C14)-aryl-(C1-C8)-alkoxy, where is also heteroaryl and aryl is optionally substituted by 1, 2 or 3 identical or different radicals from the group carboxyl, amino, nitro, C1-C4-alkylamino, C1-C6-alkoxy, hydroxyl, halogen and cyano, C1-C18-alkylmercapto, NHR3, NR3R4, a radical of the formula IV or a group which favors intracellular uptake or serves for labeling a DNA probe or, when the oligonucleotide analog hybridizes to the target nucleic acid, attacks the latter while binding, cross-linking or cleaving, and

the curved bracket indicates that R2 and the adjacent phosphoryl or —Y′—R1a radical can either be located in the 2′ and 3′ positions or else, conversely, in the 3′ and 2′ position, with it being possible for each nucleotide to be present in its D or L configuration, and for the base B to be located in the α or β position.

DETAILED DESCRIPTION

Bases which are customary in nucleotide chemistry are to be understood to mean, for example, natural bases, such as adenine, cytosine, thymine, guanine, uracil or hypoxanthine, or unnatural bases, such as, for example, purine, 8-azapurine, 2,6-diaminopurine, 7-deazaadenine, 7-deazaguanine, N4,N4-ethanocytosine, N6,N6-ethano-2,6-diaminopurine, pseudoisocytosine, 5-methylcytosine, 5-fluorouracil, 5-(C3-C6)-alkynyluracil, 5-(C3-C6)-alkynylcytosine, or their prodrug forms.

Oligonucleotides of the formula I are preferred which possess at least one 7-deazaguanine base (E is NH2 and F is OH) or 7-deazaadenine base (E is H and F is NH2) which is substituted at the 7 position.

Oligonucleotides of the formula I are particularly preferred which possess at least one 7-deazaadenine base which is substituted at the 7 position and, where appropriate, one or more 7-deazaguanine bases which are substituted at the 7 position, in addition.

Oligonucleotides of the formula I which possess at least one 7-deazapurine base which is substituted at the 7 and 8 positions (=disubstituted 7-deazapurine bases) represent a further preferred embodiment of the present invention. Oligonucleotides of the formula I having disubstituted 7-deazapurine bases are preferred in which the disubstituted 7-deazapurine bases carry a substituent at the 8 position which is defined under R16 2., 3., 4., 5., 14. and 15. A halogen, for example fluorine, is particularly preferred at the 8 position. The substituents defined under R15 3., 4., 5., 14. and 15., in particular hexynyl, are preferred substituents at the 7 position. Oligonucleotides of the formula I are also preferred in which

R15 is 1. NO2,

2. NH2,

3. —S—(C1-C6)-alkyl,

4. (C1-C6)-alkoxy,

5. (C6-C20)-aryloxy,

6. SiH3,

7.

8. (C1-C10)-alkyl, (C2-C10)-alkenyl or (C2-C10)-alkynyl which is substituted by one or more radicals from the group SH, S—(C1-C6)-alkyl, (C1-C6)-alkoxy, OH, —NR(c)R(d), —CO—R(b), —NH—CO—NR(c)R(d), —NR(c)R(g), —NR(e)R(f) or —NR(e)R(g), or by a polyalkylene glycol radical of the formula —[O—(CH2)r]s—NR(c)R(d), where r and s are, independently of each other, an integer between 1 and 18, preferably 1 and 6, with it being possible for functional groups such as OH, SH, —CO—R(b), —NH—CO—NR(c)R(d), —NR(c)R(d), —NR(e)R(f), —NR(e)R(g) or —NR(c)R(g) additionally to be linked to one or more groups, where appropriate via a further linker, which favor intracellular uptake or serve for labeling a DNA or RNA probe or, when the oligonucleotide analog hybridizes to the target nucleic acid, attack the latter while binding, cross-linking or cleaving, or

9. (C1-C10)-alkyl, (C2-C10)-alkenyl or (C2-C10)-alkynyl in which from one to all the H atoms are substituted by halogen, preferably fluorine; and

R16 is hydrogen.

If only the 7 position of the 7-deazapurine bases is substituted (R16=H), C1-C10-alkyl, C2-C10-alkenyl or C2-C10-alkynyl radicals, in which from one to all the H atoms are substituted by halogen, preferably fluorine, are then particularly preferred for the 7 position.

Generally, 7-deazapurine-containing oligonucleotides are preferred in which the 7-deazapurine bases bear electron-attracting substituents at the 7 position and/or 8 position.

Oligonucleotides of the formula I are also preferred in which the base is located in the β position on the sugar, the nucleotides are in the D configuration, R2 is located in the 2′ position and a is oxy.

The 7 position of the azapurine ring system is to be understood to mean the position at which the substituent R15 is located. Correspondingly, the substituent R16 is located at the 8 position.

When attaching to complementary nucleic acids (target nucleic acids), the novel oligonucleotides exhibit a binding affinity which is superior to that exhibited by the natural oligonucleotides.

A further advantage of the novel oligonucleotides is that their stability towards acids and nucleases is increased as compared with that of oligonucleotides which contain natural purine bases.

It is advantageous if additional modifications, for example of the phosphate backbone, the ribose unit or the oligonucleotide ends, are introduced into these oligonucleotides when they are to be used therapeutically [J. S. Cohen, Topics in Molecular and Structural Biology 12 (1989) Macmillan Press, E. Uhlmann et al., above]. For example, modifications, which are known per se, of the sugar phosphate backbone result in the novel oligonucleotides becoming even more efficiently protected against nuclease attack, which is advantageous.

Compounds of the formula I are also preferred, therefore, in which V, Y, Y′ and W have the meaning of thioxo, selenoxo, oxy, oxo, sulfanediyl, imino or methylene, and U has the meaning of hydroxyl, mercapto or methyl. These compounds are very particularly preferred if R2 additionally is hydroxyl or hydrogen, in particular hydrogen.

Compounds of the formula I in which R1 and R1a are hydrogen also represent a preferred embodiment.

Compounds of the formula I are very particularly preferred in which R1 and/or R1a is hydrogen, R2 is hydroxyl or hydrogen, U is hydroxyl or mercapto, and V, Y, Y′ and W have the meaning of thioxo, oxy, oxo or hydroxyl.

Protective groups which are customary in nucleotide chemistry are to be understood to mean, for example, amino protective groups, hydroxyl protective groups or other protective groups as described in [E. Sonveaux, 1986, Bioorganic Chemistry, 14, 274-325 or S. L. Beaucage et al., 1992, Tetrahedron, 48, 2223-2311].

Alkyl, alkenyl and alkynyl may be straight-chain or branched. The same also applies, in a corresponding manner, to radicals which are derived from them, such as alkanoyl or alkoxy. (C1-C10)-Alkyl is, in particular, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, pentyl, hexyl and heptyl. Examples of halogenated (C1-C10)-alkyls are CHF2, CF3, CH2F, CF3—CH2—CH2—, CF3—CF2—CH2, CF3(CF2)6—CH2,

Halogen is to be understood to mean iodine, bromine, chlorine or fluorine.

Heteroaryl is understood to mean, in particular, radicals which are derived from phenyl or naphthyl in which one or more CH groups are replaced by N and/or in which at least two adjacent CH groups are replaced (with the formation of a five-membered aromatic ring) by S, NH or O. In addition, one or both atoms of the condensation site of bicyclic radicals can be N atoms (as in indolizinyl). Heteroaryl is, in particular, furanyl, thienyl, pyrrolyl, imidazolyl, pyrazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, thiazolyl, isothiazolyl, pyridyl, pyrazinyl, pyrimidinyl, pyridazinyl, indolyl, indazolyl, quinolyl, isoquinolyl, phthalazinyl, quinoxalinyl, quinazolinyl and cinnolinyl.

The morpholinyl radical and the imidazolidinyl radical may be mentioned as examples of NR3R4 groups in which R3 and R4, together with the nitrogen atom carrying them, form a 5- to 6-membered heterocyclic ring which additionally contains a further heteroatom.

Physiologically tolerated salts of compounds of the formula (I) are understood to mean both inorganic and organic salts, as described in Remington's Pharmaceutical Sciences (17th edition, page 1418 (1985)).

Owing to their physical and chemical stability, and their solubility, sodium salts, potassium salts, calcium salts and ammonium salts, inter alia, are preferred for acidic groups.

The invention is not limited to α- and β-D- or L-ribofuranosides, α- and β-D- or L-deoxyribofuranosides and corresponding carbocyclic five-ring analogs, but also applies to oligonucleotide analogs which are assembled from other sugar building blocks, for example xylofuranose and arabinofuranose derivatives, ring-expanded and ring-contracted sugars, and acyclic and ring-bridged sugar derivatives or suitable sugar derivatives of a different kind. Furthermore, the invention is not limited to the derivatives of the phosphate radical which are listed by way of example in formula I, but also relates to the known dephospho derivatives.

Consequently, the novel oligonucleotides can result from modifying the natural structure in a variety of ways. Examples of such modifications, which are introduced by methods which are known per se, are:

a) Modifications of the Phosphate Bridge

The following may be mentioned by way of example: phosphorothioates, phosphorodithioates, methyl-phosphonates, phosphoroamidates, boranophosphates, methyl phosphates, ethyl phosphates and phenylphosphonates. Phosphorothioates, phosphorodithioates and methyl-phosphonates are preferred modifications of the phosphate bridge.

b) Replacement of the Phosphate Bridge

The following may be mentioned by way of example: replacement with acetamide, formacetal, 3′-thioformacetal, methylhydroxylamine, oxime, methylenedimethylhydrazo, dimethylenesulfone and silyl groups. Replacement with acetamide, formacetals and 3′-thioformacetals is preferred.

c) Modifications of the Sugar

The following may be mentioned by way of example: α-anomeric sugars, 2′-O-methylribose, 2′-O-butylribose, 2′-O-allylribose, 2′-fluoro-2′-deoxyribose, 2′-amino-2′-deoxyribose, α-arabinofuranose and carbocyclic sugar analogs. The preferred modification is that due to 2′-O-methylribose and 2′-O-n-butylribose.

d) Modifications of the Sugar and of the Phosphate Bridge

Those which may be mentioned by way of example are the peptide nucleic acids (PNA's), in which the sugar/phosphate backbone is replaced by an aminoethylglycine backbone (see German Patent Application P4408531.1), and the carbamate-bridged morpholino oligomers. The PNA's can also be linked to nucleic acids, as described in German Patent Application P4408528.1.

e) Other Modifications of the Bases, in Particular of the Pyrimidine Bases

The following may be mentioned by way of example: 5-propynyl-2′-deoxyuridine, 5-propynyl-2′-deoxycytidine, 5-hexynyl-2′-deoxyuridine, 5-hexynyl-2′-deoxycytidine, 5-fluoro-2′-deoxycytidine, 5-fluoro-2′-deoxyuridine, 5-hydroxymethyl-2′-deoxyuridine, 5-methyl-2′-deoxycytidine and 5-bromo-2′-deoxycytidine. 5-Propynyl-2′-deoxyuridine, 5-hexynyl-2′-deoxyuridine, 5-hexynyl-2′-deoxycytidine and 5-propynyl-2′-deoxycytidine are preferred modifications.

Examples of groups which favor intracellular uptake are different lipophilic radicals, such as —O—(CH2)x—CH3, in which x is an integer from 6 to 18, —O—(CH2)n—CH═CH—(CH2)m—CH3, in which n and m are, independently of each other, an integer from 6 to 12, —O—(CH2CH2O)4—(CH2)9—CH3, —O—(CH2CH2O)8—(CH2)13—CH3 and —O—(CH2CH2O)7—(CH2)15—CH3, and also steroid radicals, such as cholesteryl, or vitamin radicals, such as vitamin E, vitamin A or vitamin D, and other conjugates which exploit natural carrier systems, such as bile acid, folic acid, 2-(N-alkyl, N-alkoxy)-aminoanthraquinone and conjugates of mannose and peptides of the corresponding receptors which lead to receptor-mediated endocytosis of the oligonucleotides, such as EGF (epidermal growth factor), bradykinin and PDGF (platelet derived growth factor). Labeling groups are to be understood to mean fluorescent groups, for example of dansyl (=N-dimethyl-1-aminonaphthyl-5-sulfonyl) derivatives, fluorescein derivatives or coumarin derivatives, or chemiluminescent groups, for example of acridine derivatives, and also the digoxygenin system, which is detectable by means of ELISA, the biotin group, which is detectable by means of the biotin/avidin system, or else linker arms having functional groups which permit subsequent derivatization with detectable reporter groups, for example an amino-alkyl linker which is converted into the chemiluminescence probe using an acridinium active ester. Other suitable linkers are known to a person skilled in the art from the published patent applications EP 251786 and WO 93/09217.

h) Conjugation by way of the 7 Position and/or the 8 Position on the 7-Deazapurine

Groups which serve to label a DNA or RNA probe or which favor intracellular uptake can also be conjugated by way of the 7 position and/or 8 position of the 7-deazapurine. 7-Deazapurine nucleosides to which biotin or iminobiotin radicals are conjugated by way of the 7 position of the 7-deazapurine, via a special connecting group, have been disclosed by EP 63 879.

Labeling groups for a DNA or RNA probe are to be understood to mean fluorescent groups, for example of dansyl (=N-dimethyl-1-aminonaphthyl-5-sulfonyl) derivatives, fluorescein derivatives or coumarin derivatives, or chemiluminescent groups, for example of acridine derivatives, and also the digoxygenin system, which is detectable by means of ELISA, or the biotin group, which is detectable by means of the biotin/avidin system, and also the intercalators and chemically active groups which have already been listed under g) (see, also, Beaucage et al., Tetrah. (1993) Vol. 49, No. 10, 1925-1963). Examples of groups which favor intracellular uptake are steroid radicals, such as cholesteryl, or vitamin radicals such as vitamin E, vitamin A or vitamin D, and other conjugates which exploit natural carrier systems, such as bile acid, folic acid, 2-(N-alkyl, N-alkoxy)-aminoanthraquinone and conjugates of mannose and peptides of the corresponding receptors which lead to receptor-mediated endocytosis of the oligonucleotides, such as EGF (epidermal growth factor), bradykinin and PDGF (platelet derived growth factor).

In a general manner, the described groups can be introduced either at the level of the oligonucleotides (for example by way of SH groups) or at the level of the monomers (phosphonates, phosphoamidites or triphosphates). In the case of the monomers, in particular in the case of the triphosphates, it is advantageous to leave the side chains, into which a reporter group or an intercalator group is to be introduced, in the protected state, and only to eliminate the side-chain protective groups, and to react with an optionally activated derivative of the corresponding reporter group or intercalator group, after the phosphorylation.

R1b is a succinyl radical or other conventional linker for linking the oligonucleotide containing this group to a solid support e.g., an amino-functionalized or methylamino-functionalized support, by way of an amide or methylimide bond, or the like, or is a radical of the formula IIIc or IIId

in which

U is (C1-C18)-alkoxy, (C1-C18)-alkyl, (C6-C20)-aryl, (C6-C14)-aryl-(C1-C8)-alkyl, O—R7, S—R7 or a radical of the formula IV

(OCH2 CH2)pO(CH2)qCH2R5 (IV)

in which R5 is H;

Q is a radical —NR8R9,

R7 is —(CH2)2—CN;

R8 and R9 are identical or different and are C1-C6-alkyl, in particular isopropyl or ethyl, or, together with the nitrogen atom carrying them, are a 5-9-membered heterocyclic ring which can additionally contain a further hetero atom from the series O, S and N, in particular

E′ and F′ are, independently of each other, H, OR12 or N10R11,

R10 and R11 are identical or different and are hydrogen or an amino protective group which is customary in nucleotide chemistry, or R10 and R11 together form an amino protective group which is customary in nucleotide chemistry,

R12 is hydrogen or a hydroxyl protective group which is customary in nucleotide chemistry, such as, for example, t-butyldimethyl-silyl, dimethoxytriphenylmethyl (DMT), triisopropyl-silyl, o-nitro-benzyl, p-nitro-benzyl, iBu, 2-fluorophenyl-4-methoxypiperidin-4-yl (FPMP), or methyl,

R15 and R16 are, independently of each other,

1. hydrogen,

2. halogen,

3. (C1-C10)-alkyl,

4. (C2-C10)-alkenyl,

5. (C2-C10)-alkynyl,

6. NO2,

7. NH2,

8. cyano,

9. —S—(C1-C6)-alkyl,

10. (C1-C6)-alkoxy,

11. (C6-C20)-aryloxy,

12. SiH3,

13.

14. a radical as defined under 3., 4. or 5. which is substituted by one or more radicals from the group SH, S—(C1-C6)-alkyl, (C1-C6)-alkoxy, OH, —NR(c)R(d), —CO—R(b), —NH—CO—NR(c)R(d), —NR(c)R(g), —NR(e)R(f) or —NR(e)R(g), or by a polyalkyleneglycol radical of the formula —[O—(CH2)r]s—NR(c)R(d), where r and s are, independently of each other, an integer between 1 and 18, preferably 1 and 6, with it being possible for functional groups such as OH, SH, —CO—R(b), —NH—CO—NR(c)R(d), —NR(c)R(d), —NR(e)R(f), —NR(e)R(g) or —NR(c)R(g) to carry a protective group which is customary in nucleotide chemistry or to be linked, where appropriate via a further linker, to one or more groups which favor intracellular uptake or serve as labeling for a DNA or RNA probe or, when the oligonucleotide analog hybridizes to the target nucleic acid, attack the latter while binding, cross-linking or cleaving, or

15. a radical as defined under 3., 4. or 5. in which from one to all the H atoms are substituted by halogen, preferably fluorine.

R(a) is OH, (C1-C6)-alkoxy, (C6-C20)-aryloxy, NH2 or NH—T, where T is an alkylcarboxyl group or alkylamino group which is linked, optionally via a further linker, to one or more groups which favor intracellular uptake, or serve as labeling for a DNA or RNA probe or, when the oligonucleotide analog hybridizes to the target nucleic acid, attack the latter while binding, cross-linking or cleaving,

R(b) is hydroxyl, (C1-C6)-alkoxy or —NR(c)R(d),

R(c) and R(d) are, independently of each other, H or (C1-C6)-alkyl which is unsubstituted or substituted by —NR(e)R(f) or —NR(e)R(g),

R(e) and R(f) are, independently of each other, H or (C1-C6)-alkyl,

R(g) is (C1-C6)-alkyl-COOH, with the proviso that R15 and R16 cannot each simultaneously be hydrogen, NO2, NH2, cyano or SiH3, with functional groups such as OH, NH2 or COOH being protected, where appropriate, with a protective group which is customary in nucleotide chemistry, and the curved bracket indicating that R2b and the adjacent —Yb—R1b radical can be located in the 2′ and 3′ positions or else, conversely, in the 3′ and 2′ positions.

A preferred embodiment is represented by compounds of the formula (V) in which V, Yb and a are oxy, R2b is hydrogen or OR12, in particular hydrogen, and R1b is a radical of the formula (IIIc) or (IIId), with U being an O—(CH2)2—CN, and R8 and R9 being identical or different and being isopropyl or ethyl, or, together with the N atom carrying them, being an aliphatic heterocycle, preferably pyrrolidino. These compounds are very particularly preferred if, in addition, the base is located in the a position on the sugar and R2b is located in the 2′ position. Compounds of formula (V) are also preferred in which E is NR10R11 and F is H, and, quite generally, those compounds of the formula (V) are preferred which can be employed for preparing preferred oligonucleotides of the formula I.

The radical of the formula (IIId) which is customarily present as a salt is to be understood to mean inorganic or organic salts, for example alkali metal, alkaline earth metal or ammonium salts, which are described, for example, in Remington's Pharmaceutical. Sciences (17th edition, page 1418 (1985)). Triethylammonium and pyridinium salts may be mentioned by way of example. However, the invention also embraces compounds of the formula (V) in which the radical of the formula (IIId) is present as a free acid.

The compounds of the formula V may be employed as structural components for preparing the novel oligonucleotides of the formula I.

EP 251 786 discloses 7-deazapurine nucleotides, and their monophosphates, diphosphates or triphosphates, which possess an alkynylamino group at the 7-purine position. The alkynylamino group serves as a linker by way of which fluorescent labeling molecules can be coupled to the nucleotide. The dideoxynucleotides which have been provided with a fluorescence label can then be used as chain terminator molecules for dideoxy sequencing in accordance with Sanger and detected directly by means of fluorescence spectroscopy. U.S. Pat. No. 5,241,060 discloses 7-deazapurine nucleotides which carry a detectable radical on the 7-deazapurine.

The invention also relates to compounds of the formula VI

in which, independently of each other,

U′=U″=U′″ is hydroxyl or mercapto, and U′ can additionally be BH3,

e and f are 0 or 1;

R13 is hydrogen, OH, C1-C18-alkoxy, or C1-C6-alkenyloxy, in particular allyloxy;

E and F are, independently of each other, H, OH or NH2; and

R15 and R16 are, independently of each other,

1. hydrogen,

2. halogen,

3. (C1-C10)-alkyl,

4. (C2-C10)-alkenyl,

5. (C2-C10)-alkynyl,

6. NO2,

7. NH2,

8. cyano,

9. —S—(C1-C6)-alkyl,

10. (C1-C6)-alkoxy,

11. (C6-C20)-aryloxy,

12. SiH3,

13.

14. a radical as defined under 3., 4. or 5. which is substituted by one or more radicals from the group SH, S—(C1-C6)-alkyl, (C1-C6)-alkoxy, OH, —NR(c)R(d), —CO—R(b), —NH—CO—NR(c)R(d), —NR(c)R(g), —NR(e)R(f) or —NR(e)R(g), or by a polyalkyleneglycol radical of the formula —[O—(CH2)r]s—NR(c)R(d), where r and s are, independently of each other, an integer between 1 and 18, preferably 1 and 6, with it being possible for functional groups such as OH, SH, —CO—R(b), —NH—CO—NR(c)R(d), —NR(c)R(d), —NR(e)R(f), —NR(e)R(g) or —NR(c)R(g) additionally to be linked, where appropriate via a further linker, to one or more groups which favor intracellular uptake or serve as labeling for a DNA or RNA probe or, when the oligonucleotide analog hybridizes to the target nucleic acid, attack the latter while binding, cross-linking or cleaving, or

15. a radical as defined under 3., 4. or 5. in which from one to all the H atoms are substituted by halogen, preferably fluorine.

R(a) is OH, (C1-C6)-alkoxy, (C6-C20)-aryloxy, NH2 or NH—T, with T representing an alkylcarboxyl or alkylamino group which is linked, where appropriate via a further linker, to one or more groups which favor intracellular uptake or serve as labeling for a DNA or RNA probe or, when the oligonucleotide analog hybridizes to the target nucleic acid, attack the latter while binding, cross-linking or cleaving,

R(b) is hydroxyl, (C1-C6)-alkoxy or —NR(c)R(d),

R(c) and R(d) are, independently of each other, H or (C1-C6)-alkyl which is unsubstituted or substituted by —NR(e)R(f) or —NR(e)R(g),

R(e) and R(f) are, independently of each other, H or (C1-C6)-alkyl,

R(g) is (C1-C6)-alkyl-COOH, with the proviso that R15 and R16 cannot each simultaneously be hydrogen, NO2, NH2, cyano or SiH3, with compounds of the formula VI being excepted in which R16 is H and R15 is (C2-C10)-alkynyl which is substituted by —NR(c)R(d) or —NR(e)R(f); and with the additional proviso that e and f are not 0 if E is OH or NH2 and F is OH, R16 is hydrogen and R15 is Br, Cl, F, cyano, (C1-C4)-alkyl, (C2-C4)-alkenyl or (C2-C4)-alkynyl.

The invention also embraces compounds of the formula VI which are provided, in a generally customary manner, with a radioactive label (for example, αP atom is 32P; U′ is 35S).

Compounds of the formula VI are preferred in which U′ is hydroxyl or mercapto, U″=U′″ is hydroxyl, and e and/or f is 1. Compounds of the formula VI are particularly preferred when e and f are 1.

The compounds of the formula VI which are customarily present as a salt comprise inorganic or organic salts, for example alkali metal, alkaline earth metal or ammonium salts [Remington's Pharmaceutical Sciences (17th edition, page 1418 (1985)]. Triethylammonium and pyridinium salts may be mentioned by way of example. The novel VI compounds also comprise those compounds in which the phosphate group is present as a free acid.

The novel compounds of the formula VI may be employed generally as aids in molecular biology, for example in PCR reactions (e=f=1, R13=OH) or for sequencing (e=f=1; R13=H or OH). In PCR-reactions compounds of the formula VI are preferred in which R16 is H and R15 is halogen. Amplification of longer nucleodide sequences is enhanced using the modified oligonucleotides.

The use of the novel 7-deazapurine nucleotides for sequencing nucleic acids is advantageous for several reasons. Thus, the band compression which can often be observed in GC-rich nucleotide regions in the Sanger sequencing method (dideoxy technique), and which hinders correct determination of the nucleotide sequence, is either eliminated or at least reduced. In addition, the double-stranded nucleic acids which are synthesized by DNA polymerases or RNA polymerases during the sequencing are stabilized by the incorporation of 7-, 8- or 7,8-substituted 7-deazapurine bases. It is consequently more advantageous to use substituted 7-deazapurine nucleotides than to use unsubstituted 7-deazaguanosine nucleotides, which are customarily employed in nucleic acid sequencing in order to eliminate band compressions in GC-rich DNA stretches (EP 212536). A further advantage of using substituted 7-deazapurine nucleotides in the sequencing is that fluorescent residues in the form of reporter groups, which make possible fluorescence-spectroscopic detection of the nucleic acid molecules which are synthesized during the sequencing reaction, can be introduced onto the substituents in a series of subsequent reactions.

In addition, the incorporation of self-fluorescent, substituted 7-deazapurine bases into oligonucleotides renders it possible to detect the latter directly by way of the self-fluorescence of the substituted 7-deazapurine bases. Thus, the 7-deazapurine bases, which in unsubstituted form are not fluorescent, become fluorescent, for example, when an alkynyl group, for example hexynyl, is introduced at the 7 position. The self-fluorescence of these compounds can be measured at 350 nm (emission) following excitation with light of 280 nm wavelength.

The compounds of the formula VI can be prepared by proceeding from the corresponding substituted 7-deazapurine nucleosides and using well known methods. The compounds of the formula VI can preferably be prepared by an abbreviated one-pot method due to Ludwig, in the presence of 1,8-bis(dimethylamino)naphthalene and trimethyl phosphate [J. Ludwig et al., (1981) Acta Biochem. Biophys. Sci. Hung., 16, 131].

The invention also relates to compounds of the formula VII

in which

E and F are, independently of each other, H, OH or NH2, and OH and NH2 are, where appropriate, protected by a protective group which is customary in nucleotide chemistry;

R15 and R16 are, independently of each other, hydrogen, (C1-C10)-alkyl, (C2-C10)-alkenyl, (C2-C10)-alkynyl, I, Cl, Br, F, cyano, or (C1-C10)-alkyl, (C2-C10)-alkenyl or (C2-C10)-alkynyl in which from one to all the H atoms are substituted by halogen, preferably fluorine, with it not being possible for R15 and R16 to be simultaneously hydrogen and cyano, and with the further proviso that R15 is not I if R16 is hydrogen, E is NH2 and F is OH,

R14 are, independently of each other, H or a protective group which is customary in nucleotide chemistry.

The invention also embraces all the tautomeric forms of the compounds of the formulae I, V, VI and VII, and, in particular, all the tautomeric forms of the 7-deazapurine bases of the formula II.

In a quite general manner, those compounds of the formulae V, VI and VII are also preferred which can be used as starting compounds or intermediates for the preparation of preferred oligonucleotides of the formula I.

The invention furthermore relates to a process for preparing the novel oligonucleotides of the formula I. The standard conditions which are customary in the chemical synthesis of oligonucleotides can be applied for preparing the novel oligonucleotides containing substituted 7-deazapurine.

The novel oligonucleotides of the formula I are prepared in solution or, preferably, on a solid phase, where appropriate using an automatic synthesis device. The oligomers of the formula I can be assembled stepwise by successively condensing a mononucleotide, which in each case possesses a nucleotide base, onto an appropriately derivatized support or onto a growing oligomer chain. Alternatively, the oligonucleotides of the formula I can be assembled by joining dinucleotides or trinucleotides together [S. Beaucage et al., Tetrah. vol. 48, No. 12, 2223-2311, (1992); and Tetrah. vol. 48, No. 28, 6123-6194, (1993)]. This is particularly advantageous when synthesizing oligonucleotides which possess modified phosphate bridges.

The oligonucleotides are assembled using methods which are known to the person skilled in the art, such as the triester method, the H-phosphonate method or the phosphoramidite method [E. Sonveaux, (1986), Bioorganic Chemistry, 14, 274-325; S. L. Beaucage et al., (1992), Tetrahedron, 48, 2223-2311]. The nucleotide monomer structural components of the formula V, particularly preferably those of the formula V in which E′ is NR10R11 and F′ is OR12, or F′ is NR10NR11 and E′ is H, are preferably employed for introducing the 7-deazapurine derivatives.

The compounds of the formula V can be prepared, as structural components for the oligonucleotide solid phase synthesis, by proceeding from the corresponding 7-deazapurine nucleosides. Substituents can be introduced at the 7 position of the 7-deazapurine ring system using well-known methods. For example, the preparation of 7-deazapurine nucleosides which are substituted at the 7 position by halogen or methyl is described by Seela et al. [Helvetica Chimica Acta, (1994) 77, 897-903]. Alkenyl- or alkynyl-substituted 7-deazapurine derivatives of the formula V can be prepared by proceeding from the known 5-iodotubercidin (=7-I-7-deazaadenosine, see Seela et al., above), and coupling alkenyl or alkynyl groups onto the 7 position of the 7-deazapurine ring system by means of a cross-coupling reaction in the presence of tetrakis(triphenylphosphine)palladium(O). Electrophilic substituents (for example halogens) can be introduced into the 8 position of the 7-deazapurine ring system if nucleosides are employed as starting compounds which possess an electron-supplying substituent (for example an amino group) at the 2 position of the 7-deazapurine. If the 2-amino group is, for example, acetylated, the electrophilic substituent is then directed into the 7 position. Consequently, the present invention also relates to a process for the regioselective insertion of electrophilic substituents (for example halogens) into the 7 or 8 position of 7-deazanucleosides. The halogenated nucleosides can then be used as starting compounds for the insertion of other substituents, for example alkyl, alkenyl or alkynyl groups, by means of the above-described palladium-catalyzed cross-coupling reaction. Alkoxy derivatives or substituted amine derivatives can be introduced by nucleophilic substitution, and nitro groups can be introduced by electrophilic substitution.

After suitable protective groups for the amino groups of the 7-deazapurine bases and for the free 5′-hydroxyl group of the sugar have been introduced, the monomers are converted into the corresponding phosphonate or phosphoramidite derivatives. Suitable amino protective groups, for example in the form of a formamidine protective group ((dimethylamino)methylidene) or acyl protective groups (e.g. benzoyl or phenoxyacetyl), are inserted using well-known methods [L. J. McBride et al., (1983) Tetrahedron Lett., 24, 2953, G. S. Ti et al., (1982) J. Am. Chem. Soc., 104, 1316; H. Schaller et al. (1963), J. Am. Chem. Soc., 85, 3821], with it being advantageous, when the amino group is acylated, to use the Schaller peracylation method. An example of a suitable protective group for the free 5′-OH group of the sugar is 4,4′-dimethoxytrityl, whose insertion is likewise effected using known methods [C. B. Reese (1978), Tetrahedron, 34, 3143; D. Flockerzi et al., (1981), Liebigs Ann. Chem., 1568]. The monomers which have been protected in this way can be converted into the corresponding phosphonates in accordance with a protocol due to Froehler et al. [B. C. Froehler et al., (1986), Nucl. Acid Res., 14, 5399]. Cyanoethyl-phosphoramidite derivatives can, for example, be prepared by reacting the monomers with chloro-β-cyanoethoxy-(N,N-diisopropylamino)phosphane in anhydrous dichloromethane [N. D. Sinha et al., (1984) Nucl. Acid Res., 12, 4539].

Compounds of the formula I whose oligonucleotide moiety is modified at the 3′ end and/or the 5′ end are synthesized, as regards these modifications, using the methods described in EP-A 0 552 766.

For use according to the invention, the oligonucleotides have a length of from 4 to 100, preferably of about 5-40, in particular of about 6-30, nucleotides. Otherwise, the above-described preference ranges, modifications and conjugations also apply in this case too.

The present invention relates to the use of oligonucleotides containing at least one substituted 7-deazapurine, preferably 7-deazaadenine or 7-deazaguanine, as a diagnostic reagent, for example for detecting the presence or absence of, or the quantity of, a specific double-stranded or single-stranded nucleic acid molecule in a biological sample. One or more of these oligonucleotides maybe directly or indirectly bound or absorbed onto a solid support, or provided as a solution in a solvent or diluent, optionally together with other conventional diagnostically relevant auxiliary reagents.

The invention furthermore relates to pharmaceutical compositions comprising one or more oligonucleotides of the formula I, together with a physiologically acceptable excipient and, where appropriate, suitable additives and/or conventional auxiliary substances.

In a quite general manner, the present invention extends to the use of oligonucleotides of the formula I in therapeutically effective amounts in improved therapeutic methods. In general, therapeutically effective oligonucleotide derivatives are understood to mean antisense oligonucleotides, triple helix-forming oligonucleotides, aptamers or ribozymes, in particular antisense oligonucleotides.

The pharmaceuticals of the present invention can, for example, be used to treat diseases which are caused by viruses, for example by HIV, HSV-1, HSV-2, influenza, VSV, hepatitis B or papilloma viruses.

Novel antisense oligonucleotide derivatives, that is antisense oligonucleotides in which at least one purine base is replaced by a substituted 7-deazapurine base, and which are effective against these targets, have, for example, the following base sequences:

a) against HIV, e.g.

5′-ACACCCAATTCTGAAAATGG-3′ (SEQ ID NO: 1) or (I)

5′-AGGTCCCTGTTCGGGCGCCA-3′ (SEQ ID NO: 2) or (II)

5′-GTCGACACCCAATTCTGAAAATGGATAAA-3′ (SEQ ID NO: 3) (III)

5′-GCTATGTCGACACCCAATTCTGAAA-3′ (SEQ ID NO: 4) or (IV)

5′-TCGTCGCTGTCTCCGCTTCTTCTTCCTGCCA-3′ (SEQ ID NO: 5) or (VI)

b) against HSV-1, e.g.

5′-GCGGGGCTCCATGGGGGTCG-3′ (SEQ ID NO: 6) (VII)

The pharmaceuticals of the present invention are also suitable, for example, for treating cancer. For example, oligonucleotide sequences can be used in this context which are directed against targets which are responsible for the occurrence of cancer or for cancer growth. Examples of such targets are:

Novel antisense oligonucleotides of the formula I which are effective against these targets have, for example, the following base sequences:

a) against c-Ha-ras, e.g.

5′-CAGCTGCAACCCAGC-3′ (SEQ ID NO: 7) (VIII)

c) c-myc, e.g.

5′-GGCTGCTGGAGCGGGGCACAC-3′ (SEQ ID NO: 8) (IX)

5′-AACGTTGAGGGGCAT-3′ (SEQ ID NO: 9) (X)

d) c-myb, e.g.

5′-GTGCCGGGGTCTTCGGGC-3′ (SEQ ID NO: 10) (XI)

e) c-fos, e.g.

5′-GGAGAACATCATGGTCGAAAG-3′ (SEQ ID NO: 11) (XII)

5′-CCCGAGAACATCATGGTCGAAG-3′ (SEQ ID NO: 12) (XIII)

5′-GGGGAAAGCCCGGCAAGGGG-3′ (SEQ ID NO: 13) (XIV)

f) p120, e.g.

5′-CACCCGCCTTGGCCTCCCAC-3′ (SEQ ID NO: 14) (XV)

g) EGF receptor, e.g.

5′-GGGACTCCGGCGCAGCGC-3′ (SEQ ID NO: 15) (XVI)

5′-GGCAAACTTTCTTTTCCTCC-3′ (SEQ ID NO: 16) (XVII)

h) p53 tumor suppressor, e.g.

5′-GGGAAGGAGGAGGATGAGG-3′ (SEQ ID NO: 17) (XVIII)

5′-GGCAGTCATCCAGCTTCGGAG-3′ (SEQ ID NO: 18) (XIX)

The pharmaceuticals of the present invention are furthermore suitable, for example, for treating diseases which are affected by integrins or cell-cell adhesion receptors, for example by VLA-4, VLA-2, ICAM, VCAM or ELAM.

Novel antisense oligonucleotide derivatives which are effective against these targets have, for example, the following base sequences:

a) VLA-4, e.g.

5′-GCAGTAAGCATCCATATC-3′ (SEQ ID NO: 19) or (XX)

b) ICAM, e.g.

5′-CCCCCACCACTTCCCCTCTC-3′ (SEQ ID NO: 20) (XXI)

5′-CTCCCCCACCACTTCCCCTC-3′ (SEQ ID NO: 21) (XXII)

5′-GCTGGGAGCCATAGCGAGG-3′ (SEQ ID NO: 22) (XXIII)

c) ELAM-1, e.g.

5′-ACTGCTGCCTCTTGTCTCAGG-3′ (SEQ ID NO: 23) (XXIV)

5′-CAATCAATGACTTCAAGAGTTC-3′ (SEQ ID NO: 24) (XXV)

The pharmaceuticals of the present invention are also suitable, for example, for preventing restenosis. For example, oligonucleotide sequences can be used in this context which are directed against targets which are responsible for proliferation or migration. Examples of these targets are:

Novel oligonucleotides of the formula I which are effective against these targets have, for example, the following base sequences:

a) c-myb

5′-GTGTCGGGGTCTCCGGGC-3′ (SEQ ID NO: 25) (XXVI)

b) c-myc

5′-CACGTTGAGGGGCAT-3′ (SEQ ID NO: 26) (XXVII)

c) cdc2 kinase

5′-GTCTTCCATAGTTACTCA-3′ (SEQ ID NO: 27) (XXVIII)

d) PCNA (proliferating cell nuclear antigen of rat)

5′-GATCAGGCGTGCCTCAAA-3′ (SEQ ID NO: 28) (XXIX)

The pharmaceuticals can be used, for example, in the form of pharmaceutical preparations which can be administered orally, for example in the form of tablets, coated tablets, hard or soft gelatin capsules, solutions, emulsions or suspensions. The inclusion of the pharmaceuticals in liposomes, which, where appropriate, contain additional components such as proteins, likewise represents a suitable administration form. They can also be administered rectally, for example in the form of suppositories, or parenterally, for example in the form of injection solutions. For the production of pharmaceutical preparations, these compounds can be processed in therapeutically inert, organic and inorganic excipients. Examples of such excipients for tablets, coated tablets and hard gelatin capsules are lactose, corn starch, or derivatives thereof, tallow and stearic acid, or salts thereof. Suitable excipients for preparing solutions are water, polyols, sucrose, invert sugar and glucose. Suitable excipients for injection solutions are water, alcohols, polyols, glycerol and vegetable oils. Suitable excipients for suppositories are vegetable and hardened oils, waxes, fats and semiliquid polyols. The pharmaceutical preparations can also contain preservatives, solvents, stabilizers, wetting agents, emulsifiers, sweeteners, colorants, flavorants, salts for altering the osmotic pressure, buffers, coating agents, antioxidants and other therapeutical active compounds, where appropriate.

Preferred forms of administration are topical administrations, local administrations, such as, for example, using a catheter, or else injections. For injection, the antisense oligonucleotide derivatives are formulated in a liquid solution, preferably in a physiologically acceptable buffer, such as, e.g., Hank's solution or Ringer's solution. However, the antisense oligonucleotides can also be formulated in solid form and dissolved or suspended prior to use. The doses which are preferred for systemic administration amount to from about 0.01 mg/kg to about 50 mg/kg of body weight and per day.

In a quite general manner, the invention extends to the use of compounds of the formula I as DNA probes or primers in DNA diagnostics and, in a general manner, as aids in molecular biology , as noted earlier.

Individual DNA molecules can be visualized electron microscopically, for example in a scanning-tunneling microscope. While pyrimidine bases can be differentiated electronmicroscopically due to the methyl group at the 5 position, this is not possible in the case of the purine bases adenine and guanine. It is not possible, therefore, to decode the base sequences of nucleic acid molecules electronmicroscopically in a straightforward manner. However, if the nucleic acid molecule to be investigated now contain substituted 7-deazaguanine derivatives, for example, in place of the unmodified guanine bases, the substituted 7-deazaguanine bases can be distinguished in the electron microscope from unsubstituted adenine bases (and, conversely, guanine bases can be distinguished from substituted 7-deazaadenine bases). Consequently, the base sequences of nucleic acids which contain 7-substituted 7-deazapurine bases can be decoded by electron microscopy.

EXAMPLES

The compounds (1)-(25) named in the examples exhibit the following structural formulae.

1.14 g (4.0 mmol) of 5-chlorodeoxytubercidin (1) are evaporated twice with dry pyridine and dissolved in 10 ml of dry pyridine, and this solution is then stirred, at room temperature for 2 h, together with 5.2 ml (40.6 mmol) of trimethylchlorosilane. 520 μl (4.1 mmol) of freshly distilled benzoyl chloride are then added, and the mixture is stirred at room temperature for a further 2 h. 4 ml of water and, after a further 5 min, 8 ml of 25% aqueous ammonia are added dropwise while cooling with ice. The mixture is stirred at room temperature for 30 min and then evaporated to dryness. The residue is taken up in 20 ml of water, and this solution is extracted three times with 30 ml of ethyl acetate on each occasion. The organic phases are dried over Na2SO4 and evaporated, and the residue is chromatographed on silica gel (20×5 cm column, dichloromethane/methanol 9:1). 930 mg (2.4 mmol, 60%) of the compound (4) are obtained, as colorless crystals, from the more slowly migrating main fraction after evaporating the solvent and recrystallizing the residue from methanol/water: m.p. 190° C.

1.31 g (4.0 mmol) of 5-bromodeoxytubercidin (2) are evaporated twice with dry pyridine and dissolved in 10 ml of dry pyridine, and this solution is then stirred, at room temperature for 2 h, together with 5.2 ml (40.6 mmol) of trimethylchlorosilane. 520 μl (4.1 mmol) of freshly distilled benzoyl chloride are then added and the mixture is stirred at room temperature for a further 2 h. 4 ml of water and, after a further 5 min, 8 ml of 25% aqueous ammonia are added dropwise while cooling with ice. The mixture is stirred at room temperature for 30 min and then worked up in analogy with compound 14b. 1.2 g (2.8 mmol, 70%) of colorless crystals, of m.p. 198° C., are obtained after chromatography on silica gel (20×5 cm column, dichloromethane/methanol 9:1), evaporation of the solvent and recrystallization from methanol/water.

1.06 g (4.0 mmol) of 5-methyldeoxytubercidin (3) are reevaporated twice with 20 ml of absolute pyridine on each occasion and dissolved in 10 ml of dry pyridine, and this solution is stirred, at room temperature, for 2 h, together with 5.2 ml (40.6 mmol) of trimethylchlorosilane. 520 μl (4.1 mmol) of freshly distilled benzoyl chloride are then added, and the mixture is stirred at room temperature for a further 2 h. The working-up is carried out in analogy to that for compound (4), and chromatography then takes place on silica gel (20×5 cm column, dichloromethane/methanol 9:1). 1.1 g (2.9 mmol, 73%) of colorless crystals (compound 6), with a m.p. of 196° C., are obtained from the more slowly migrating main fraction after evaporating the solvent and recrystallizing from methanol/water.

1.5 ml (8.75 mmol) of N,N-dimethylformamide diethyl acetal are added to a solution of 200 mg (0.61 mmol) of the compound (2) in 15 ml of dimethylformamide, and the reaction solution is left to stir at room temperature for 2 h. It is then concentrated down to dryness, and the oily residue is reevaporated twice with toluene and twice with acetone. The crude product is adsorbed on silica gel and purified by column chromatography (20×5 cm column, dichloromethane/methanol 9:1). Compound (7) is obtained, as colorless platelets (150 mg, 0.4 mmol, 65%): m.p. 177° C., after concentrating the main fraction and recrystallizing the residue from acetone/methanol 9:1.

500 mg (1.28 mmol) of compound (4) are evaporated twice with dry pyridine and then dissolved in 20 ml of absolute pyridine. 650 mg (1.95 mmol) of dimethoxytrityl chloride are added, and the mixture is stirred at room temperature for 1 h. It is then hydrolyzed with 10 ml of a 5% aqueous solution of NaHCO3 and extracted twice with 25 ml of dichloromethane on each occasion. After the combined organic phases have been dried over Na2SO4, chromatography takes place on silica gel (20×5 cm column, dichloromethane/methanol 9:1). The residue which is obtained after inspissating the main zone yields, after evaporating with acetone, 680 mg (0.99 mmol, 77%) of a yellowish foam. For the purification, the substance is dissolved in a little dichloromethane, and this solution is slowly added dropwise, while stirring vigorously, to a 200-fold excess of n-hexane. Compound (8) is isolated as a white, amorphous solid.

500 mg (1.15 mol) of compound (5) are evaporated twice with dry pyridine and subsequently dissolved in 20 ml of absolute pyridine. 585 mg (1.75 mmol) of dimethoxytrityl chloride are added, and the mixture is stirred at room temperature for 1 h. It is then hydrolyzed with 10 ml of a 5% aqueous solution of NaHCO3 and extracted twice with 25 ml of dichloromethane on each occasion. After the combined organic phases have been dried over Na2SO4, chromatography takes place on silica gel (20×5 cm column, dichloromethane/methanol 9:1). The residue which is obtained after inspissating the main zone yields, after evaporating with acetone, 620 mg (0.93 mmol, 80%) of a yellowish foam. For the purification, the substance is dissolved in a little dichloromethane and this solution is slowly added dropwise, while stirring vigorously, to a 200-fold excess of n-hexane. Compound (9) precipitates out as a white amorphous solid and is filtered off with suction.

500 mg (1.36 mmol) of compound (6) are evaporated twice with 20 ml of dry pyridine on each occasion and dissolved in 20 ml of absolute pyridine, and this solution is stirred, at room temperature for 1 h, together with 690 mg (2.1 mmol) of dimethoxytrityl chloride. The mixture is worked up in an analogous manner to that employed for compound (8), and chromatographed on silica gel (20×5 cm column, dichloromethane/methanol 9:1). 720 mg (1.05 mmol, 77%) of the completely protected compound (10) are obtained, as a yellowish foam, from the main zone. Purification, by reprecipitating from n-hexane, yields a colorless, amorphous solid.

840 mg (12.0 mmol) of 1,2,4-1H-triazole are added, at room temperature and under an argon atmosphere, to a solution of 315 μl (3.7 mmol) of phosphorus trichloride and 4.1 ml (37.0 mmol) of N-methylmorpholine in 40 ml of absolute dichloromethane. After the mixture has been stirred for 30 minutes, it is cooled down to 0° C. and a solution of 500 mg (0.74 mmol) of the fully protected nucleoside (8) in 10 ml of dry dichloromethane is added dropwise over a period of 10 min. The mixture is left to stir at room temperature for a further 10 min, and 30 ml of 1 M triethylammonium bicarbonate buffer (TBC, pH=7.5) are then added. The phases are separated and the aqueous phase is extracted several times with CH2Cl2; the combined organic phases are then dried over Na2SO4. The solvent is evaporated off and the remaining foam is chromatographed on silica gel (20×5 cm column, 0.5 l dichloromethane/Et3N 98:2, and then dichloromethane/methanol/Et3N 88:10:2). After the main zone has been concentrated, the residue is taken up in 50 ml of dichloromethane and this solution is extracted five times with 25 ml of 0.1 M TBC buffer on each occasion. 445 mg (0.52 mmol, 70%) of the phosphonate (11) are obtained, as a colorless foam, after drying the organic phase over Na2SO4 and evaporating off the solvent. For the further purification, this foam is reprecipitated from n-hexane in an analogous manner to that used for the fully protected nucleoside (8).

770 mg (11.0 mmol) of 1,2,4-1H-triazole are added, at room temperature and under an argon atmosphere, to a solution of 290 μl (3.4 mmol) of phosphorus trichloride and 3.8 ml (34.0 mmol) of N-methylmorpholine in 30 ml of absolute dichloromethane. After the mixture has been stirred for 30 minutes, it is cooled down to 0° C. and a solution of 500 mg (0.68 mmol) of the completely protected nucleoside (9) in 10 ml of dry dichloromethane is added dropwise within the space of 10 min. The mixture is left to stir at room temperature for a further 10 min and 30 ml of 1 M triethylammonium bicarbonate buffer (TBC, pH=7.5) are then added. The phases are separated, the aqueous phase is extracted several times with CH2Cl2, and the combined organic phases are dried over Na2SO4. The solvent is evaporated off and the remaining foam is chromatographed on silica gel (20×5 cm column, 0.5 l of dichloromethane/Et3N, 98:2, and, after that, dichloromethane/methanol/Et3N, 88:10:2). After the main zone has been concentrated, the residue is taken up in 50 ml of dichloromethane and this solution is extracted five times with 25 ml of 0.1 M TBC buffer on each occasion. 410 mg (0.46 mmol, 67%) of the phosphonate (12) are obtained as a colorless foam after the organic phase has been dried over Na2SO4 and the solvent has been evaporated off. For the further purification, this foam can be reprecipitated from n-hexane in an analogous manner to that for the completely protected nucleoside (9).

0.78 g (11.3 mmol) of 1,2,4-H-triazole are added, at room temperature and under an argon atmosphere, to a solution of 25 ml of absolute dichloromethane, 290 μl (3.4 mmol) of phosphorus trichloride and 3.44 g (34.0 mmol) of N-methylmorpholine. After it has been stirred for 30 minutes, the reaction solution is cooled down to 0° C. and a solution of 500 mg (0.75 mmol) of the fully protected nucleoside (10) in 15 ml of dichloromethane is added within the space of 10 min. The mixture is allowed to stir at room temperature for a further 20 min and is then hydrolyzed with 1 M triethylammonium bicarbonate buffer (TBC, pH=7.5). After the phases have been separated, the aqueous phase has been extracted three times with 20 ml of dichloromethane on each occasion, and the organic phase has been dried and concentrated by evaporation, the residue is chromatographed on silica gel (20×5 cm column, 0.5 1 l of dichloromethane/Et3N, 98:2, and, after that, dichloromethane/methanol/Et3N, 88:10:2). The main zone is inspissated and the residue is taken up in 50 ml of dichloromethane and this solution is extracted several times with 0.1 M TBC buffer. 440 mg (0.53 mmol, 70%) of the compound (13) are obtained as a colorless foam after drying the organic phase over Na2SO4 and evaporating off the solvent.

Compound (2) (33 mg, 0.1 mmol) is dissolved, together with 1,8-bis(dimethylamino)naphthalene (33 mg, 0.15 mmol), in trimethyl phosphate (0.25 ml) while warming gently. After the solution has been cooled down to 0° C., freshly distilled POCl3 (12 μl, 0.13 mmol) is added. The reaction mixture is maintained at 4° C. for 4 h and a solution comprising tri-n-butylammonium diphosphate (0.5 m in DMF, 1 ml) and tri-n-butylamine (100 μl, 0.42 mmol) is then added. After the mixture has been stirred at 0° C. for 3 min, 1 M TBC buffer (10 ml) is added and the whole is evaporated to dryness. The residue is chromatographed on DEAD Sephadex (1.5×20 cm column, HCO3− form). After washing the column with approximately 500 ml of H2O, chromatography took place using a linear gradient of H2O/0.9 M TBC buffer (1 l in each case). During this procedure, the triphosphate (0.019 mM, 20%) is obtained at approximately 0.5 M TBC buffer.

5-Iodo-2′-deoxytubercidin (14) (200 mg, 0.532 mmol) and copper(I) iodide (10 mg, 10 mol %) are suspended in 3 ml of dry DMF, which has been previously flushed with argon, and alkyne (6-15 eq.), dry triethylamine (108 mg, 1.06 mmol, 2 eq.) and tetrakis(triphenylphosphine)palladium (0) (30.75 mg, 0.027 mmol, 5 mol %) are added to this mixture. Within a few hours, the mixture turns into a clear yellow solution. The reaction is continued until the starting compounds are used up (monitoring by thin layer chromatography). The reaction mixture is then diluted with 5 ml of methanol/dichloromethane (1:1), and Dowex 1×8 (100-200 mesh; 500 mg, bicarbonate form) is added. Once the gas formation has ceased, after 15 minutes of stirring, the reaction mixture is stirred for a further 30 minutes. It is then filtered and the matrix is washed with methanol/dichloromethane (1:1). The filtrates are combined and dried. The dried residue is immediately chromatographed on a silica gel column (25 g) using dichloromethane having an increasing content of methanol (10, 15, 20%). The substituted 2′-deoxytubercidin derivative is obtained after evaporating the main fraction.

The Dmt-hydroxyl protective group is inserted into 4-benzoylamino-5-(1-propynyl-3-trifluoroacetamide)-7-[(2-deoxy-β-D-erythropentofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine in analogy with Example 5.

d) The Title Compound (15) is Prepared From 4-Benzoylamino-5-(1-propynyl-3-trifluoroacetamide)-7-[(2-deoxy-β-D-erythropentofuranosyl)-5′-O-(4,4′-dimethoxytriphenylmethyl)]-7H-pyrrolo[2,3-d]pyrimidine in Analogy With Example 8.

7-(2-Deoxy-β-D-erythropentofuranosyl)-4-methoxy-2-[(formyl)amino]-7H-pyrrolo[2,3-d]pyrimidine (1.0 g, 3.3 mmol) [F. Seela, H. Driller, Nucleosides, Nucleotides 1989, 8, 1-21] in acetonitrile (20 ml) was stirred, at room temperature for 15 hours, together with isobutyric anhydride (33 mmol) in the presence of triethylamine (23 mmol). The solvent is evaporated off and the residue is reevaporated with methanol. It is then chromatographed in the eluent methylene chloride/acetone (95:5), and the main zone is isolated and the constituent compound is recrystallized from cyclohexane. 1.26 g (89%) of a colorless solid.

A solution of compound 18 (10.1 mmol) in dimethylformamide was stirred, at room temperature for 1 hour, together with N-bromosuccinimide (10.1 mmol). A few drops of 5% aqueous NaHCO3 are added to the solution, in order to buffer it, and methylene chloride is then added. The organic phase is shaken with water, separated, dried over sodium sulfate and evaporated. Chromatography of the residue on a silica gel column in the eluent dichloromethane/acetone (95:5) results in two zones. The evaporation residue from the slowly migrating main zone yields colorless (19) (75%) as a solid.

Using N-chlorosuccinimide, the substance was prepared and worked up in analogy with compound (19). The halogenation reaction time was 8 hours. Acetonitrile/DMF (4:1) was used as the solvent. Colorless solid (70%).

The compound 5,6-dichloro-7-[2-deoxy-3,5-di-O-(2-methylpropionyl)-β-D-erythropentofuranosyl]-4-methoxy-2-amino-7H-pyrrolo[2,3-d]pyrimidine, in the form of a colorless solid, was obtained as a by-product.

Compound (19) is reacted using a known method [F. Seela, B. Westermann, U. Bindig, J. Chem. Soc. Perkin Trans I 1988, 699]. 500 mg of compound (19) are heated under reflux for 3 hours in 200 ml of 2 N NaOH. The cooled solution is neutralized with glacial acetic acid, the inorganic residue is filtered off, and the aqueous phase is evaporated. Recrystallization from water results in colorless crystals of (21).

36.6 mg (0.27 mmol) of N-chlorosuccinimide are added to a solution of 50 mg (0.14 mmol) of 2-amino-7-(2-deoxy-3,5-di-O-acetyl-β-D-erythropentofuranosyl)-4-methoxy-7H-pyrrolo[2,3-d]pyrimidine in 3 ml of dichloromethane, and the mixture is stirred at room temperature for 12 h. The solvent is stripped off and the residue is chromatographed on silica gel in CH2Cl2/acetone (9:1). 30 mg (54%) of a colorless foam are obtained from the slowly migrating main zone.

The corresponding 5-thiocyanate derivative is formed by proceeding from 2′,3′,5′-tri-O-acetyl-7-deazaadenosine and reacting this compound with thiocyanogen chloride in acetic acid. Reduction with 2-mercaptoethanol and subsequent methylation yields the 5-methylthio derivative having an unprotected sugar residue (Watanabe et al., Nucleosides & Nucleotides, 1 (2), 191-203, 1982). The methylthio compound (32) is obtained by selective silylation of the 3′,5′-OH groups and subsequent Barton deoxygenation by way of the corresponding thionoester.

(33) can be prepared by using the Mannich reaction. The 5-morpholinomethyl derivative (Watanabe et al., Nucleosides & Nucleotides, 1(2), 191-203, 1982) is obtained by heating tubercidin together with paraformaldehyde and morpholine in DMF. The 5-morpholine derivative (33) is obtained in accordance with the silylation and deoxygenation described in Ex. 33.

Example 67Solid Phase Synthesis of the Oligodeoxyribonucleotides by the Phosphonate Method

The oligodeoxyribonucleotide syntheses were carried out on a 1 μmol scale on a solid phase (CPG: ®Controlled Pore Glass) in an automated model 380 B DNA synthesizer (Applied Biosystems, Weiterstadt) by means of the phosphonate technique, with the DNA fragment being synthesized in the 3′-5′ direction. The reaction cycle (detritylation, coupling, capping and oxidation) followed a program which was developed for phosphonate chemistry [H. Köster, K. Kulikowsky, T. Liese, W. Heikens, V. Kohli, Tetrahedron 1981, 37, 363]. The base-protected oligonucleotide, whose 5′-hydroxyl group was also protected by Dmt, was cleaved from the support within 30 min using 25% aqueous ammonia. The protective groups on the heterocycles were removed at 60° C. in the same medium within 48 h. While adding a drop of triethylamine (to avoid premature elimination of the 5′-OH protective group) the samples were concentrated down to about 200 μl in a Speed-Vac ®concentrator. In this state, they can be kept at −25° C. for some months.

Example 68Solid Phase Synthesis of the Oligodeoxyribonucleotides by the Phosphoramidite Method

The oligodeoxyribonucleotide syntheses were carried out on a 1 μmol scale in an automated model 380 B DNA synthesizer (Applied Biosystems, Weiterstadt) by means of the solid phase phosphoramidite technique using ®CPG (controlled pore glass) or ®Fractosil to which the first nucleoside unit is bonded via its 3′ end. The following steps were carried out:

1. Washing with abs. acetonitrile,

2. treating with 3% trichloroacetic acid in dichloromethane,

3. washing with abs. acetonitrile,

4. condensing with 10 μmol of 5′-O-dimethoxytritylnucleoside-3′-β-cyanoethyl phosphite-diisopropylamidite and 50 μmol of tetrazole in 0.3 ml of abs. acetonitrile,

Steps 1 to 8, termed a DNA reaction cycle below, were repeated in order to assemble the oligonucleotide in accordance with the sequence to be synthesized, with the 5′-O-dimethoxytrityl(nucleotide base)-3′-β-cyanoethylphosphite-diisopropylamidite, which in each case corresponded to the sequence, being employed in step 4. Once the synthesis is complete, working-up is carried out as described in Example 67.

Example 69HPLC Purification of the Trityl-protected and Deprotected Oligonucleotides

In the first purification step, the DMT-protected oligomers were purified by HPLC on RP-18 silica gel (eluent system I, see below), evaporated to dryness, reevaporated several times with dry methanol, and subsequently detritylated, while cooling with ice, by 10-minute exposure to 80% strength acetic acid. After that, the acid was neutralized dropwise with triethylamine (1-2 ml) at 0° C., concentrated almost to dryness and then reevaporated twice with absolute methanol. After the residue had been taken up in 500 μl of double-distilled water, the completely deprotected oligonucleotides were once again purified by HPLC on RP-18 silica gel (eluent system II, see below). The combined main zones were evaporated and the residue was dissolved in 500 μl of double-distilled water, and this solution was desalted through a short RP-18 column (eluent system III, see below). After having been lyophilized in a Speed-Vac concentrator, the oligonucleotides were taken up in 100 μl of double-distilled water and this solution was stored at −25° C.

The following HPLC eluents were used:

A: 0.1 M triethylammonium acetate, pH 7.0/5% strength acetonitrile

B: double-distilled water

C: acetonitrile

D: methanol/water, 3:2

The following gradient systems, composed of the above eluents, were employed:

Example 70Characterization of the Oligodeoxyribonucleotides by Means of Enzymic Hydrolysis

The oligonucleotides (0.5 A260 units in each case) are dissolved in 0.1 M tris-HCl buffer (pH=8.3, 200 μl) and incubated with snake venom phosphodiesterase (3 μg) at 37° C. for 45 min. Alkaline phosphatase (3 μg) is then added and the temperature is maintained at 37° C. for a further 30 min. The resulting nucleoside mixture is analyzed by means of UV spectrophotometry using reversed-phase HPLC (eluent system V). The nucleoside composition of the corresponding oligonucleotide can be quantified on the basis of the peak areas and the extinction coefficients of the nucleosides at 260 nm (dA: 15400, dC: 7300, dG: 11700, dT: 8800, Brdc7A: 5300, Medc7A: 4900, Cldc7A: 6300).

Example 71Determination of Cleavage Hypochromicity by Means of the Enzymic Hydrolysis of the Oligonucleotides

0.2 A260 units of the oligonucleotide are hydrolyzed with snake venom phosphodiesterase in 0.1 M tris-HCl buffer (pH=8.3, 200 μl). From the UV absorption at 260 nm before and after cleaving, the hypochromicity in % can be calculated, while taking into account the enzyme absorption, in accordance with the following equation:

Henzyme=[(εmonomer−εpolymer)×(εmonomer)−1]×100%

Example 72UV-spectroscopic and CD-spectroscopic Determination of the Tm Values and Calculation of the Thermodynamic Data

The Tm values of the oligomers were determined using a Cary 1 UV-Vis spectrophotometer (Varian, Melbourne, Australia). The temperature was varied linearly by 0.5° C. or 1.0° C. per minute. In order to investigate the melting temperature, oligomer concentrations of between 0.2 and 0.8 A260 units in 1 ml of 60 mM sodium cacodylate buffer (pH 7.5, 1 M NaCl, 100 mM MgCl2) were used. In the experiments on the non-self-complementary oligonucleotides, the single-strand concentration was 0.2-0.6 OD. The melting hypochromicity in % is obtained from the difference in absorption before and after melting in accordance with the following equation:

Hmelt.=[(Ae−At)Ae−1]×100

The melting curves were analyzed using a program based on a two-state model (“stacked/unstacked”) in accordance with the equation:

ln K=ln[(ES−E)/(EU−E)]=S/R−H/RT

where E=absorption at the corresponding wavelength, S=stacked and U=unstacked. The temperature-dependent CD spectra were plotted in a wavelength range of 200-350 nm using a Jasco 600 spectropolarimeter with a thermostated quartz cuvette. The temperature was increased in intervals of 5-10° C. in a range of from 5-80° C. at concentrations of from 3 to 15 μM in 60 mM Na cacodylate buffer and at 0.1 M, 1 and 4 M NaCl.

0.5 A260 units of the appropriate oligonucleotide are dissolved in 100 μl of buffer (composed of 50 μM tris-HCl buffer, pH 7.5, 100 mM NaCl, 10 mM magnesium chloride and 1 mM dithioerythritol), and EcoRI endodeoxyribonuclease (high concentration, 5 μl≡250 units) is added to this solution. The mixture was then incubated at 37° C. and samples of in each case 10 μl in volume were removed at 30 min intervals and analyzed by reverse-phase HPLC (eluent system II).

Example 75Testing for Nuclease Stability

10 nmol of the oligonucleotide to be investigated are dissolved in 450 μl of 20% strength fetal calf serum in RPMI medium and 50 μl of double-distilled water, and this solution is incubated at 37° C. 10 μl samples for gel electrophoresis or 20 μl samples for HPLC are then removed immediately and after 1, 2, 4, 7 and 24 hours; the reaction is terminated by adding 5 μl of 10 μl of formamide and heating at 95° C. for 5 minutes. For the gel electrophoresis, the samples are loaded onto a 15% polyacrylamide gel (2% BIS), which is developed at about 3000 volt hours. The bands are visualized by silver staining. For the HPLC analysis, the samples are injected onto a Gen-Pak fax HPLC column (Waters/Millipore) and chromatographed at 1 ml/min using from 5 to 50% buffer A in B (buffer A: 10 mM sodium dihydrogen phosphate, 0.1 H NaCl in acetonitrile/water, 1:4 (v:v) pH 6.8; buffer B: as A, but containing 1.5 M NaCl).

Example 76Testing for Antiviral Activity

The antiviral activity of the test substances against various herpes viruses whch are pathogenic to humans is examined in a cell culture test system. For the experiment, monkey kidney cells (Vero, 2×105/ml) in serum-containing Dulbecco's MEM (5% fetal calf serum, FCS) are sown in 96-well microtiter plates, which are incubated at 37° C. for 24 h in 5% CO2. The serum-containing medium is then sucked off and the cells are rinsed twice with serum-free Dulbecco's MEM (-FCS). The test substances are prediluted in H2O to a concentration of 600 μM and stored at −18° C. Further dilution steps in Dulbecco's minimal essential medium (MEM) are carried out for the test. 100 μl of each of the individual test substance dilutions are added, together with 100 μl of serum-free Dulbecco's MEM (-FCS), to the rinsed cells. After having been incubated at 37° C. for 3 h in 5% CO2, the cells are infected with herpes simplex virus type 1 (ATCC VR733, HSV-1 F strain) or with herpes simplex virus type 2 (ATCC VR734, HSV-2 G strain) in concentrations at which the cell lawn is completely destroyed within 3 days. In the case of HSV-1, the infection intensity is 500 plaque-forming units (PFU) per well, and in the case of HSV-2 it is 350 PFU/well. The experimental mixtures then contain test substance at concentrations of from 80 μM to 0.04 μM in MEM, supplemented with 100 U/ml penicillin G and 100 mg/l streptomycin. All the experiments are carried out as duplicate determinations apart from the controls, which are carried out eight times per plate. The experimental mixtures are incubated at 37° C. for 17 h and in 5% CO2. The cytotoxicity of the test substances is determined after a total incubation time of 20 h by microscopic assessment of the cell cultures. The highest preparation concentration which still does not cause any microscopically recognizable cell damage under the specified experimental conditions is designated the maximum tolerated dose (MTD). FCS is then added to a final concentration of 4% and the plates are incubated at 37° C. in 5% CO2 for a further 55 h. The untreated infection controls then exhibit a fully developed cytopathic effect (CPE). After the cell cultures have been assessed microscopically, they are stained with neutral red using Finter's (1966) vital staining method. The antiviral activity of a test substance is defined as the minimum inhibitory concentration (MIC) which is required in order to protect 30-60% of the cells from the cytopathic effect of the virus.